DNA methylation contributes to natural human variation
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ABSTRACT:
PROVIDER: PRJNA153243 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Natural DNA methylation variation was examined in a population of wild Lotus japonicus accessions from Japan
2017-06-01 | GSE78767 | GEO
Project description:Widespread natural variation of DNA methylation within angiosperms
| PRJNA316109 | ENA
Project description:DNA methylation analysis using the Infinium HumanMethylation450 BeadChip platform (Illumina) of 96 Caucasian American, 96 Han Chinese American and 96 African American LCL samples determined differences in terms of differentially methylated sites. Importantly, the observed differences were confirmed in primary blood samples of 10 healthy Caucasian, 10 African American (GSE36064) and 10 Asian individuals. Genes associated to differentially methylated site suggest an influence of DNA methylation on phenotype differences. Interestingly, methylation differences could be partially traced back to genetic polymorphisms. DNA was quantified by Quant-iT PicoGreen dsDNA Reagent (Invitrogen) and the integrity was analyzed in a 1.3% agarose gel. Bisulfite conversion of 600 ng of each sample was perform according to the manufacturer's recommendation for Illumina Infinium Assay. Effective bisulphite conversion was checked for three controls that were converted simultaneously with the samples. 4 ul of bisulfite converted DNA were used to hybridize on Infinium HumanMethylation 450 BeadChip, following Illumina Infinium HD Methylation protocol. Chip analysis was performed using Illumina HiScan SQ fluorescent scanner. The intensities of the images are extracted using GenomeStudio (2010.3) Methylation module (1.8.5) software. Methylation score of each CpG is represented as beta value.
2013-07-22 | E-GEOD-36369 | biostudies-arrayexpress
Project description:DNA methylation analysis using the Infinium HumanMethylation450 BeadChip platform (Illumina) of 96 Caucasian American, 96 Han Chinese American and 96 African American LCL samples determined differences in terms of differentially methylated sites. Importantly, the observed differences were confirmed in primary blood samples of 10 healthy Caucasian, 10 African American (GSE36064) and 10 Asian individuals. Genes associated to differentially methylated site suggest an influence of DNA methylation on phenotype differences. Interestingly, methylation differences could be partially traced back to genetic polymorphisms.
2013-07-22 | GSE36369 | GEO
Project description:DNA methylation is a chemical modification of DNA that can be faithfully inherited across generations in flowering plant genomes. Failure to properly maintain DNA methylation can lead to epigenetic variation and transposon reactivation. Plant genomes are dynamic, spanning large ranges in size and there is an interplay between the genome and epigenome in shaping one another. To understand the variation in genomic patterning of DNA methylation between species, we compared methylomes of numerous diverse angiosperm species. By examining these variations in a phylogenetic context it becomes clear that there is extensive variation in mechanisms that govern gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. Extensive variation is observed at all cytosine sequence contexts (CG, CHG and CHH, where H = A, C, T), with the Brassicaceae showing reduced CHG methylation levels and also reduced or loss of CG gene-body methylation. The Poaceae are characterized by a lack or reduction of heterochromatic CHH methylation and enrichment of CHH methylation in genic regions. Reduced CHH methylation levels are found in clonally propagated species, suggesting that these methods of propagation may alter the epigenomic landscape over time, in the absence of sexual reproduction. These results show that DNA methylation targeting pathways have diverged functionally and that extant DNA methylation patterns are likely a reflection of the evolutionary and life histories of plant species.
2016-09-02 | GSE79526 | GEO
Project description:DNA methylation is a chemical modification of DNA that can be faithfully inherited across generations in flowering plant genomes. Failure to properly maintain DNA methylation can lead to epigenetic variation and transposon reactivation. Plant genomes are dynamic, spanning large ranges in size and there is an interplay between the genome and epigenome in shaping one another. To understand the variation in genomic patterning of DNA methylation between species, we compared methylomes of numerous diverse angiosperm species. By examining these variations in a phylogenetic context it becomes clear that there is extensive variation in mechanisms that govern gene body DNA methylation, euchromatic silencing of transposons and repeats, as well as silencing of heterochromatic transposons. Extensive variation is observed at all cytosine sequence contexts (CG, CHG and CHH, where H = A, C, T), with the Brassicaceae showing reduced CHG methylation levels and also reduced or loss of CG gene-body methylation. The Poaceae are characterized by a lack or reduction of heterochromatic CHH methylation and enrichment of CHH methylation in genic regions. Reduced CHH methylation levels are found in clonally propagated species, suggesting that these methods of propagation may alter the epigenomic landscape over time, in the absence of sexual reproduction. These results show that DNA methylation targeting pathways have diverged functionally and that extant DNA methylation patterns are likely a reflection of the evolutionary and life histories of plant species. Bisulfite-seq of leaf tissue from plants representing diverse angiosperms. RNA-seq and small RNA-seq was performed on leaf tissue of a subset of the species.
2016-09-02 | E-GEOD-79526 | biostudies-arrayexpress
Project description:DNA methylation patterns are important for establishing cell, tissue, and organism phenotypes, but little is known about their contribution to natural human variation. To determine their contribution to variability, we have generated genome-scale DNA methylation profiles of three human populations (Caucasian-American, African-American, and Han Chinese-American) and examined the differentially methylated CpG sites. The distinctly methylated genes identified suggest an influence of DNA methylation on phenotype differences, such as susceptibility to certain diseases and pathogens, and response to drugs and environmental agents. DNA methylation differences can be partially traced back to genetic variation, suggesting that differentially methylated CpG sites serve as evolutionarily established mediators between the genetic code and phenotypic variability. Notably, one-third of the DNA methylation differences were not associated with any genetic variation, suggesting that variation in population-specific sites takes place at the genetic and epigenetic levels, highlighting the contribution of epigenetic modification to natural human variation.
| S-EPMC3759714 | biostudies-literature
Project description:Anopheles natural genome variation
| PRJEB2141 | ENA
Project description:DNA methylation is a chromatin modification that contributes to epigenetic regulation of gene expression. The inheritance patterns and trans-generational stability of 962 differentially methylated regions (DMRs) were assessed in a panel of 71 near-isogenic lines (NILs) derived from maize (Zea mays) inbred lines B73 and Mo17. The majority of DMRs exhibit inheritance patterns that would be expected for local (cis) inheritance of DNA methylation variation such that DNA methylation level was coupled to local genotype. There are few examples of DNA methylation that exhibit trans-acting control or paramutation-like patterns. The cis-controlled DMRs provided an opportunity to study the stability of inheritance for DNA methylation variation. There was very little evidence for alterations of DNA methylation levels at the cis-controlled DMRs during NIL population development. DNA methylation level was associated with local genotypes in all of the >30,000 examined cases except one. Additionally, the majority of the DMRs were not associated with small RNA. Together, our results suggest that a significant portion of DNA methylation variation in maize exhibits cis-controlled inheritance patterns, is highly stable and does not require active programming by small RNAs for maintenance. Methylation profiles in seedling tissue of maize near-isogenic lines (NILs) derived from B73 and Mo17 using a custom 12x270K NimbleGen array.
2014-04-01 | E-GEOD-51567 | biostudies-arrayexpress
Project description:DNA methylation is a chromatin modification that contributes to epigenetic regulation of gene expression. The inheritance patterns and trans-generational stability of 962 differentially methylated regions (DMRs) were assessed in a panel of 71 near-isogenic lines (NILs) derived from maize (Zea mays) inbred lines B73 and Mo17. The majority of DMRs exhibit inheritance patterns that would be expected for local (cis) inheritance of DNA methylation variation such that DNA methylation level was coupled to local genotype. There are few examples of DNA methylation that exhibit trans-acting control or paramutation-like patterns. The cis-controlled DMRs provided an opportunity to study the stability of inheritance for DNA methylation variation. There was very little evidence for alterations of DNA methylation levels at the cis-controlled DMRs during NIL population development. DNA methylation level was associated with local genotypes in all of the >30,000 examined cases except one. Additionally, the majority of the DMRs were not associated with small RNA. Together, our results suggest that a significant portion of DNA methylation variation in maize exhibits cis-controlled inheritance patterns, is highly stable and does not require active programming by small RNAs for maintenance.
2014-04-01 | GSE51567 | GEO